Quantitative Proteomics for Xenopus Embryos II, Data Analysis.

TitleQuantitative Proteomics for Xenopus Embryos II, Data Analysis.
Publication TypeJournal Article
Year of Publication2018
AuthorsSonnett, M, Gupta, M, Nguyen, T, Wühr, M
JournalMethods Mol Biol
Date Published2018
KeywordsAnimals, Cluster Analysis, Data Analysis, Embryo, Nonmammalian, Gene Ontology, Humans, Mass Spectrometry, Peptides, Proteome, Proteomics, Time Factors, Xenopus laevis, Xenopus Proteins

<p>The oocytes, embryos, and cell-free lysates of the frog Xenopus laevis have emerged as powerful models for quantitative proteomic experiments. In the accompanying paper (Chapter 13) we describe how to prepare samples and acquire multiplexed proteomics spectra from those. As an illustrative example we use a 10-stage developmental time series from the egg to stage 35 (just before hatching). Here, we outline how to convert the ~700,000 acquired mass spectra from this time series into protein expression dynamics for ~9000 proteins. We first outline a preliminary quality-control analysis to discover any errors that occurred during sample preparation. We discuss how peptide and protein identification error rates are controlled, and how peptide and protein species are quantified. Our analysis relies on the freely available MaxQuant proteomics pipeline. Finally, we demonstrate how to start interpreting this large dataset by clustering and gene-set enrichment analysis.</p>

Alternate JournalMethods Mol Biol
PubMed ID30151768
PubMed Central IDPMC6534117
Grant ListF31 GM116451 / GM / NIGMS NIH HHS / United States
R35 GM128813 / GM / NIGMS NIH HHS / United States